Initial commit

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

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+Package: climateR
+Type: Package
+Title: What the Package Does (Title Case)
+Version: 0.1.0
+Author: Who wrote it
+Maintainer: The package maintainer <[email protected]>
+Description: More about what it does (maybe more than one line)
+    Use four spaces when indenting paragraphs within the Description.
+License: What license is it under?
+Encoding: UTF-8
+LazyData: true

LICENSE

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+MIT License
+
+Copyright (c) 2018 mikejohnson51
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

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+exportPattern("^[[:alpha:]]+")

R/climateMeta.R

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+climate = list(
+
+macaV2metdata = list(
+  PARAM = data.frame(
+    parameter = c('tasmax','tasmin','rhsmax',
+                  'rhsmin','pr','rsds',
+                  'uas','vas','huss'),
+
+    longname = c(   'Maximum daily temperature near surface',
+                    'Minimum daily temperature near surface',
+                    'Maximum daily relative humidity near surface',
+                    'Minimum daily relative humdity near surface',
+                    'Average daily precipitation amount at surface',
+                    'Average daily downward shortwave radiation at surface',
+                    'Average daily eastward component of wind near surface',
+                    'Average daily northward component of wind near surface',
+                    'Average daily specific humidity near surface'),
+
+    units = c("K", "K", "%", "%", "mm", "W m-2", "m s-1", "m s-1", "kg kg-1"),
+
+    scale_factor = c(0.1, 0.1, 1, 1, 0.1, 1, 0.1, 0.1, 1.0E-5),
+     stringsAsFactors = F
+  ),
+
+  models = data.frame(
+  name = c("bcc-csm1-1",     "bcc-csm1-1-m",   "BNU-ESM",        "CanESM2",
+             "CCSM4",          "CNRM-CM5",       "CSIRO-Mk3-6-0",  "GFDL-ESM2M",
+             "GFDL-ESM2G",     "HadGEM2-ES",     "HadGEM2-CC",     "inmcm4",
+             "IPSL-CM5A-LR",   "IPSL-CM5A-MR",   "IPSL-CM5B-LR",   "MIROC5",
+             "MIROC-ESM",      "MIROC-ESM-CHEM", "MRI-CGCM3",   "NorESM1-M" ),
+
+ country = c("China",          "China",          "China",          "Canada",
+             "USA",            "France",        "Australia",      "USA",
+             "USA",            "United Kingdom", "United Kingdom", "Russia",
+             "France",        "France",         "France",         "Japan",
+             "Japan",          "Japan",          "Japan",          "Norway" ),
+
+ agency = c("Beijing Climate Center, China Meteorological Administration",
+   "Beijing Climate Center, China Meteorological Administration",
+   "College of Global Change and Earth System Science, Beijing Normal University, China",
+   "Canadian Centre for Climate Modeling and Analysis",
+   "National Center of Atmospheric Research, USA",
+   "National Centre of Meteorological Research, France",
+   "Commonwealth Scientific and Industrial Research Organization/Queensland Climate Change Centre of Excellence, Australia",
+   "NOAA Geophysical Fluid Dynamics Laboratory, USA",
+   "NOAA Geophysical Fluid Dynamics Laboratory, USA",
+   "Met Office Hadley Center, UK",
+   "Met Office Hadley Center, UK",
+   "Institute for Numerical Mathematics, Russia",
+   "Institut Pierre Simon Laplace, France",
+   "Institut Pierre Simon Laplace, France",
+   "Institut Pierre Simon Laplace, France",
+   "Atmosphere and Ocean Research Institute (The University of Tokyo),\n\t\tNational Institute for Environmental Studies,and Japan Agency for Marine-Earth Science and Technology",
+   "Japan Agency for Marine-Earth Science and Technology, Atmosphere and Ocean Research Institute (The University of Tokyo), and National Institute for Environmental Studies",
+   "Japan Agency for Marine-Earth Science and Technology, Atmosphere and Ocean Research Institute (The University of Tokyo), and National Institute for Environmental Studies",
+   "Meteorological Research Institute, Japan",
+   "Norwegian Climate Center, Norway"),
+
+ AtmoRes_lonlat = c("2.8 deg x 2.8 deg",  "1.12 deg x 1.12 deg",
+               "2.8 deg x 2.8 deg",   "2.8 deg x 2.8 deg",
+               "1.25 deg x 0.94 deg", "1.4 deg x 1.4 deg",
+               "1.8 deg x 1.8 deg",   "2.5 deg x 2.0 deg",
+               "2.5 deg x 2.0 deg",   "1.88 deg x 1.25 deg",
+               "1.88 deg x 1.25 deg", "2.0 deg x 1.5 deg",
+               "3.75 deg x 1.8 deg",  "2.5 deg x 1.25 deg",
+               "2.75 deg x 1.8 deg",  "1.4 deg x 1.4 deg",
+               "2.8 deg x 2.8 deg",   "2.8 deg x 2.8 deg",
+               "1.1 deg x 1.1 deg",   "2.5 deg x 1.9 deg"),
+
+ensemble = c( "r1i1p1", "r1i1p1", "r1i1p1", "r1i1p1", "r6i1p1",
+              "r1i1p1", "r1i1p1", "r1i1p1", "r1i1p1", "r1i1p1",
+              "r1i1p1", "r1i1p1", "r1i1p1", "r1i1p1", "r1i1p1",
+              "r1i1p1", "r1i1p1", "r1i1p1", "r1i1p1", "r1i1p1"),
+stringsAsFactors = FALSE),
+
+secenarios = c('rcp45', 'rcp85'),
+
+metadata = data.frame(res = '4km',
+                        spatialExtent = "Contiguous USA",
+                        dataum = "WGS 84",
+                        startDate = "2006-01-01",
+                        endData = "2099-12-31",
+                        leapDays = 'Yes',
+                        stringsAsFactors = F)
+
+
+),
+
+
+# UofI Data ---------------------------------------------------------------
+
+
+UofIMETDATA = list(
+  PARAM = data.frame(
+param = c('precipitation_amount',
+          'max_air_temperature',
+          'min_air_temperature',
+          'surface_downwelling_shortwave_flux_in_air',
+          'specific_humidity',
+          'max_relative_humidity',
+          'min_relative_humidity',
+          'wind_speed'),
+
+description = c('precipitation',
+                'maximum temperature',
+                'minimum temperature',
+                'downward shortwave solar radiation',
+                'specific humidity',
+                'maximum relative humidity',
+                'minimum relative humidity',
+                'wind speed'),
+
+unit = c('mm', 'K', 'K', 'W m-2', 'kg/kg', '%', '%', 'm/s'),
+
+scale_factor = c(0.1, 0.1, 0.1, 0.1, 0.001, 0.1, 0.1, 0.1), stringsAsFactors = TRUE
+)
+)
+)
+
+

R/getGridded.R

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+#' Get NWM gridded data output
+#'
+#' Download land output from the HydroShare Thredds server for a list of input files.
+#' Parallized version of \code{get_land_data} using \code{doParallel} and \code{foreach}.
+#'
+#' @param AOI a AOI to subset data (generated with AOI::getAOI())
+#' @param filelist a list of filepaths (generated with getFiles)
+#' @param param a channel paramater
+#' @param layer for soil and snow land parameters a layer must be declared (defaults to 1)
+#'
+#' @return a raster stack
+#' @export
+#'
+
+getGridded = function(AOI, filelist, param, layer = NULL) {
+
+  i = NULL
+
+  types  = c("channel", "land", "forcing", "terrain", "reservoir")
+
+  type = types[sapply(types, grepl, filelist[1])]
+
+  if(type == 'terrain') { param = tolower(param)} else { param = toupper(param) }
+
+  `%dopar%` <- foreach::`%dopar%`
+
+  combine_lists <- function(LL1, LL2) {
+    r <- raster::stack(LL1$r, LL2$r)
+    time <- c(LL1$time, LL2$time)
+    return(list(r = r, time = time))
+  }
+
+  layer = defineLayers(param, layer)
+
+  grid = define_AOI_grid(AOI)
+
+  no_cores <- parallel::detectCores() - 1
+  doParallel::registerDoParallel(no_cores)
+
+  res <-
+    foreach::foreach(i = 1:length(filelist) , .combine = combine_lists) %dopar% {
+
+      file = paste0(filelist[i],
+                    "?time[0:1:0],",
+                    param,
+                    "[0:1:0][",
+                    grid$y.min,
+                    ":1:",
+                    grid$y.max ,
+                    "]",
+                    layer$layer.p,
+                    "[",
+                    grid$x.min,
+                    ":1:",
+                    grid$x.max,
+                    "]"
+      )
+
+      nc = ncdf4::nc_open(file)
+      vals = ncdf4::ncvar_get(nc, param)
+      time = ncdf4::ncvar_get(nc, "time")
+      ncdf4::nc_close(nc)
+
+      mat <- apply(t(vals),2,rev)
+      r <-raster::raster(mat)
+      raster::projection(r) = sp::CRS("+proj=lcc +lat_1=30 +lat_2=60 +lat_0=40 +lon_0=-97 +x_0=0 +y_0=0 +a=6370000 +b=6370000 +units=m +no_defs")
+      raster::extent(r) = c(grid$long.min, grid$long.max, grid$lat.min, grid$lat.max)
+      raster::res(r) = 1000
+
+      return(list(r = r, time = time))
+
+    }
+
+  names(res$r) <- paste0("X.", res$time)
+
+  return(res$r)
+
+}

R/getMACA.R

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+getMACA = function(AOI, param, model, scenario, sdate, edate = NULL, write.path = "/Users/mikejohnson/Documents/WRF_Hydro/output/"){
+
+base = "https://cida.usgs.gov/thredds/dodsC/macav2metdata_daily_future?"
+
+if(is.null(edate)){edate = sdate}
+dates = seq.Date(as.Date(sdate, format = "%Y-%m-%d", tz = 'GMT' ), as.Date(edate, format = "%Y-%m-%d", tz = 'GMT' ) , by = 1)
+dates = dates - as.Date("2006-01-01", format = "%Y-%m-%d", tz = 'GMT')
+
+nc = ncdf4::nc_open(paste0(base, "lon,lat"))
+lat = ncdf4::ncvar_get(nc, "lat")
+lon = ncdf4::ncvar_get(nc, "lon")
+ncdf4::nc_close(nc)
+
+min.lat = which.min(abs(lat-min(AOI@bbox[2,])))
+max.lat = which.min(abs(lat-max(AOI@bbox[2,])))
+
+min.lon = which.min(abs(lon-min(AOI@bbox[1,])))
+max.lon = which.min(abs(lon-max(AOI@bbox[1,])))
+
+l = list(base =  paste0(param, "_",
+                model, "_r1i1p1_",
+                scenario),
+
+         call =  paste0("[", dates[1] , ":1:", tail(dates, 1), "]",
+                "[", min.lat , ":1:", max.lat, "]",
+                "[", min.lon , ":1:", max.lon, "]")
+)
+
+xx = paste(do.call(paste0,l), collapse = ",")
+
+xx = paste0( xx , ",time[",dates[1], ":1:", tail(dates, 1), "],lat[", min.lat , ":1:", max.lat, "],", "lon[", min.lon , ":1:", max.lon, "]")
+
+r = ncdf4::nc_open(paste0(base, xx))
+
+return(r)
+}
+
+
+
+
+
+
+
+
+
+
+
+

R/getRaster.R

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+getRaster = function(r){
+xx = names(r$var)
+nc = r
+
+no_cores <- parallel::detectCores() - 1
+doParallel::registerDoParallel(no_cores)
+
+res <-
+  foreach::foreach(i = 1:length(xx) , .combine = raster::stack) %dopar% {
+
+    vals = ncdf4::ncvar_get(nc, xx[i])
+
+    mat <- apply(t(vals),2,rev)
+    r <-raster::raster(mat)
+    raster::projection(r) = sp::CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
+    raster::extent(r) = c(lon[min.lon], lon[max.lon], lat[min.lat], lat[max.lat])
+    names(r) = xx[i]
+
+    return(r)
+
+  }
+
+}
+